Merge branch 'main' into breakdown-rfe-protocolunit

openfe/protocols/openmm_rfe/equil_rfe_methods.py

@@ -3,7 +3,7 @@
 """Equilibrium Relative Free Energy Protocol using OpenMM and OpenMMTools in a
 Perses-like manner.
 
-This module implements the necessary tooling to run calculate the
+This module implements the necessary tooling to calculate the
 relative free energy of a ligand transformation using OpenMM tools and one of
 the following methods:
     - Hamiltonian Replica Exchange

openfe/protocols/openmm_rfe/hybridtop_protocols.py

@@ -275,14 +275,13 @@ def _validate_mapping(
 
         # check that the mapping components are in the alchemical components
         for m in mapping:
-            if m.componentA not in alchemical_components["stateA"]:
-                raise ValueError(
-                    f"Mapping componentA {m.componentA} not in alchemical components of stateA"
-                )
-            if m.componentB not in alchemical_components["stateB"]:
-                raise ValueError(
-                    f"Mapping componentB {m.componentB} not in alchemical components of stateB"
-                )
+            for state in ["A", "B"]:
+                comp = getattr(m, f"component{state}")
+                if comp not in alchemical_components[f"state{state}"]:
+                    raise ValueError(
+                        f"Mapping component{state} {comp} not "
+                        f"in alchemical components of state{state}"
+                    )
 
         # TODO: remove - this is now the default behaviour?
         # Check for element changes in mappings
@@ -350,7 +349,7 @@ def _equal_charges(moli, molj):
 
         if len(clashes) > 0:
             errmsg = (
-                "Found SmallMoleculeComponents are are isomorphic "
+                "Found SmallMoleculeComponents that are isomorphic "
                 "but with different charges, this is not currently allowed. "
                 f"Affected components: {clashes}"
             )
@@ -384,6 +383,8 @@ def _validate_charge_difference(
             nonbonded method is not PME.
           * If the absolute charge difference is greater than one
             and an explicit charge correction is attempted.
+          * If an explicit charge correction is attempted and there is no
+            solvent present.
         UserWarning
           * If there is any charge difference.
         """
@@ -404,7 +405,7 @@ def _validate_charge_difference(
             return
 
         if solvent_component is None:
-            errmsg = "Cannot use eplicit charge correction without solvent"
+            errmsg = "Cannot use explicit charge correction without solvent"
             raise ValueError(errmsg)
 
         # We implicitly check earlier that we have to have pme for a solvated
@@ -515,7 +516,7 @@ def _validate(
         # Validate the end states
         self._validate_endstates(stateA, stateB)
 
-        # Valildate the mapping
+        # Validate the mapping
         alchem_comps = system_validation.get_alchemical_components(stateA, stateB)
         self._validate_mapping(mapping, alchem_comps)
 

openfe/protocols/openmm_rfe/hybridtop_units.py

@@ -22,7 +22,7 @@
 import matplotlib.pyplot as plt
 import mdtraj
 import numpy as np
-import numpy.typing as npt
+import numpy.typing as nptnpt
 import openmm
 import openmmtools
 from gufe import (

openfe/tests/protocols/openmm_rfe/test_hybrid_top_validation.py

@@ -353,7 +353,7 @@ def test_charge_difference_no_corr(benzene_to_benzoic_mapping):
 
 
 def test_charge_difference_no_solvent(benzene_to_benzoic_mapping):
-    errmsg = "Cannot use eplicit charge correction without solvent"
+    errmsg = "Cannot use explicit charge correction without solvent"
 
     with pytest.raises(ValueError, match=errmsg):
         openmm_rfe.RelativeHybridTopologyProtocol._validate_charge_difference(